The RNA world strikes again

Life is said to have originated in the RNA world.  We all know about the big 3 important RNAs for the cell, mRNA, ribosomal RNA and transfer RNA.  But just like the water, sewer, power and subway systems under Manhattan, there is another world down there in the cell which is just beginning to come into focus

I’ve written several posts about the RNA world in our cells (links at the end), but the latest is really staggering, in that RNA is helping to organize the how our DNA lies in the nucleus.

As usual the discoveries depended new technologies — RD-SPRITE in this case (you don’t want to know what the acronym stands for (by the bye have you noticed how many more acronyms are appearing in papers you read?).  It is extremely complex, but the technique is said to be able to simultaneously map thousands of  RNA and DNA molecules at high resolution relative to all other RNA and DNA molecules.  Details in Cell vol. 184 pp. 5775 – 5790 ’21 .

The count of long nonCoding (for protein that is) RNAs is now in the tens of thousands [ Science vol. 373 pp. 623 – 624 ’21 ]. They have all sorts of functions, but the present work shows that 93% of them stay close to the gene that transcribes them in the nucleus.  Here they bind other proteins in precise territories in the nucleus (because the gene for lncRNAs are found in territories as precise  in the nucleus).   This establishes functional compartments in the nucleus to regulate gene expression.

Interestingly long nonCoding RNAs are transcribed at very low levels, which led people to dismiss them as chaff.  By binding proteins this explains how so few molecules can do so much.

That’s pretty abstract.  Consider Xist, a large nonCoding RNA which inactivates one of the X chromosomes in females.  Just two xists are able to seed a multiprotein cloud around the Xist locus on the X.

Later to be described is Jpx which is crucial in establishing TADs (topologically associated domains)

Here are some older posts on the RNA world

Forgotten but not gone

Forgotten but not gone — take II

Forgotten but not gone — take III

Back to the drawing board on knockouts and knockdowns

Nothing could be simpler than the distinction between the initial product of genes that code for proteins (mRNA) and genes that don’t (long non-Coding RNAs — aka lncRNA, lincRNA). Not anymore according to an exceedingly clever and well thought out piece of work.

[ Cell vol. 168 pp. 753 – 755, 843 – 855 ’17 ] We know that ultraviolet light damages DNA primarily by forming pyrimidine dimers. Naturally transcription of DNA won’t be as accurate, so the cell has ways to shut it down. Ultraviolet exposure results in an unusual type of restriction of transcription along with slower elongation, with the result that only the promoter proximal 20 – 25 kiloBases of a protein coding gene are efficiently transcribed into mRNA.

In addition, after ultraviolet damage there is a global switch in pre-mRNA processing resulting in a preference for the production of transcripts containing alternative last exons not normally included in the dominant mRNA isoform. Some 84 genes are processed this way.

ASCC3 is the strongest regulator of transcription following UV damage, acting to repress it after UV damage. It is a DEAD/DEAH box DNA helicase component. The ASCC3 protein interacts with RNA polymerase II (Pol II) and becomes highly ubiquitinated and phosphorylated on UV irradiation. It isn’t required to establish transcriptional repression, just maintainance. Disruption of the UV specific form — e.g. the short isoform containing the alternative last exon has the opposite effect, allowing transcriptional recovery after UV damage.

This explains why the human genes remaining expressed (or actually induced) after UV irradiation are invariably ‘very short’ (whatever that means).

The short and long isoforms constitute an autonomous regulatory module, and are related functionally, so the effect of deleting one can at least be partially compensated for by deleting the other.

The 3,100 nucleotide long ‘short’ isoform, codes for a protein, but the protein itself didn’t have the effect of the short form mRNA (see if you can figure out, without reading further how the authors proved this). The mRNA produced from the short isoform is found almost exclusively in the nucleus. The authors put in a stop codon immediately downstream of the start codon which ablated protein production but not transcription into the appropriate mRNA, but there was still rescue of the transcriptional recovery phenotype. So the functional form of the short RNA isoform is mediated by a nonCoding RNA encoded in the ASCC3 protein coding gene. The short ASCC3 isoform has an open reading frame of 333 nucleotides, but functionally it is a lncRNA (of 3.5 kiloBases).

So protein genes can produce functional lncRNAs. How many of them actually do this is unknown. When you knockdown a gene, how much of the effect is due to less protein and how much due to the (putative) lncRNA which also might be produced by the gene. That’s why it’s back to the drawing board for knockout mice (or even mRNA knockdown using shRNA etc. etc.)

The current definition of lncRNA is absence of protein coding potential in a gene.

Why have the same gene code for two different things — there may be a regulatory advantage — controlling the function of the protein. lncRNAs have the unique ability to act in close spatial proximity to their transcription loci.

Stay tuned. It’s just fascinating what we still don’t know.